When you want to freeze the sauerkraut to keep it longer it should still retain the healthy probiotics.
The freezing temperatures do not usually kill off the good bacteria or probiotics in the sauerkraut so you'll usually still get the same health benefits from the sauerkraut when frozen as well.
It's usually the heating process of the sauerkraut or cooking sauerkraut that kills off the probiotics or when you pasteurize the sauerkraut like some store bought sauerkraut does.
But just freezing the homemade sauerkraut should not kill off the good bacteria or probiotics so it should still retain the health benefits.